Attendees & Time
Sarah, Michael M, Ryan, Magdalena, Peter, Kong, Jens, Dahlia, John
Date: April 2nd, 2010. 1:05 pm.
- deleted unused things
- cleaned up code
- streamlined call graph
- single mode gone (use version 188.8.131.52)
- contact scoring gone
- precalculate various grid terms
2. DOCK 184.108.40.206 improvements
- chem.bmp bumping instead of distmap contact bumping
- new hierarchy code (should eliminate some broken)
- no more out of bounds molecules
- no more clashing molecules
- deprecated unused keywords (more later)
- vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
- 64bit/32bit builds (use dock.csh instead of calling directly)
- speedups (3-5x)
3. Deprecated keywords
4. New keywords
- keyword default suggested
- remove_positive_solvation no YES
- check_clashes yes YES
- it is great
All of this is live since Mar 18 2010 in dock72!
Sarah raised the issue of the flexible protein code of Niu Huang:
- Is it compatible with the current improvements? <math>\rightarrow</math> probably not.
- Is anybody using it?
- Would it be worth it to update and include it?
- Can it be used in an automatic fashion, e.g. for DOCK Blaster?
- How can we predict water positions and usefulness (maybe initial water placement with PLOP)?
<math>\Rightarrow</math> who will be doing all of this?
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